BioPython Pairwise2 vs. COBALT - what's the difference?

Question

[ngarber]

I've started using BioPython's pairwise2.align module to align protein homologs. But in my pre-programming days, I was used to doing this with COBALT.

It looks like one difference is that Pairwise2 only accepts two sequences, whereas COBALT accepts an unlimited number of sequences for comparison. Is that the only practical difference, or are there other differences?

Answer 1

[Istvan Albert]

These are two different methodologies altogether.

A pairwise aligner aligns two sequences where the optimal, highest-scoring pair is the resulting alignment.

A multiple sequence aligner aligns multiple sequences simultaneously, but none of the pairwise alignements may be the optimal, highest scoring. Overall, the sum of scores over all the alignments may be optimal.

[ngarber]

This was the answer I was looking for - thanks!